The D3100 would probably be better (quality wise) than a D90 for video. The D3100 shoots full 1080p, while the D90's stuck at 720, and although the D90 offers better control, you final result would probably be better on the D3100. The D7000 would be the compromise between the two, it would offer the D90's control, and even better IQ (image quality) than the D3100. If you're mainly doing video, AF shouldn't matter to you so much, so I don't see the reason of needing the built in AF motor (if you do need the AF, perhaps just sell the old 50 and buy the newer AF-S version).
In summary, if you want the control and quality, save up and go for the D7000, but if you can live without the extra control then perhaps just sell your 50mm, and replace it with the newer version that will AF.
And by the way, you should have all of the manual controls on the D90.
Gear: 7 Nikon Nikkor AI-S and AF-S lenses, SB-700 flash, Nikon D7000, Nikon FM, variety of accessories
"There are no rules for good photographs, there are only good photographs."
- Ansel Adams